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Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-18 Balaka Mondal, Debayan Chakraborty, Naoto Hori, Hung T. Nguyen, D. Thirumalai
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Enhanced Twist-Averaging Technique for Magnetic Metals: Applications Using Quantum Monte Carlo J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-18 Abdulgani Annaberdiyev, Panchapakesan Ganesh, Jaron T. Krogel
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Systematic QM/MM Study for Predicting 31P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-18 Judit Katalin Szántó, Johannes C. B. Dietschreit, Mikhail Shein, Anne K. Schütz, Christian Ochsenfeld
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Folded Spectrum VQE: A Quantum Computing Method for the Calculation of Molecular Excited States J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-16 Lila Cadi Tazi, Alex J. W. Thom
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Score Dynamics: Scaling Molecular Dynamics with Picoseconds Time Steps via Conditional Diffusion Model J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-15 Tim Hsu, Babak Sadigh, Vasily Bulatov, Fei Zhou
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Performance of Density Functionals for Excited-State Properties of Isolated Chromophores and Exciplexes: Emission Spectra, Solvatochromic Shifts, and Charge-Transfer Character J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-15 Abhilash Patra, George Baffour Pipim, Anna I. Krylov, Shaama Mallikarjun Sharada
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Consistent Construction of the Density Matrix from Surface Hopping Trajectories J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-15 Jiabo Xu, Zhecun Shi, Linjun Wang
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Structural Coarse-Graining via Multiobjective Optimization with Differentiable Simulation J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-14 Zhenghao Wu, Tianhang Zhou
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Three-Center Tight-Binding Together with Multipolar Auxiliary Functions J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-14 Maxime Van den Bossche
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Optimizing Shot Assignment in Variational Quantum Eigensolver Measurement J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-14 Linghua Zhu, Senwei Liang, Chao Yang, Xiaosong Li
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Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-13 Kristian Kříž, Paul J. van Maaren, David van der Spoel
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Floquet Engineering of a Diatomic Molecule through a Bichromatic Radiation Field J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-13 Edgar Barriga, Luis E. F. Foa Torres, Carlos Cárdenas
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Acceleration of Solvation Free Energy Calculation via Thermodynamic Integration Coupled with Gaussian Process Regression and Improved Gelman–Rubin Convergence Diagnostics J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-12 Zhou Yu, Enrique R. Batista, Ping Yang, Danny Perez
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Basis Set Requirements of σ-Functionals for Gaussian- and Slater-Type Basis Functions and Comparison with Range-Separated Hybrid and Double Hybrid Functionals J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-11 Steffen Fauser, Arno Förster, Leon Redeker, Christian Neiss, Jannis Erhard, Egor Trushin, Andreas Görling
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Comprehensive Analysis of Coupled Proline Cis–Trans States in Bradykinin Using ωBP-REMD Simulations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-11 Maximilian Kienlein, Martin Zacharias, Maria M. Reif
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Machine Learning Isotropic g Values of Radical Polymers J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-08 Davis Thomas Daniel, Souvik Mitra, Rüdiger-A. Eichel, Diddo Diddens, Josef Granwehr
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The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-07 Tosaporn Sattasathuchana, Peng Xu, Colleen Bertoni, Yu Lim Kim, Sarom S. Leang, Buu Q. Pham, Mark S. Gordon
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High-Performance Multi-GPU Analytic RI-MP2 Energy Gradients J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-08 Ryan Stocks, Elise Palethorpe, Giuseppe M. J. Barca
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Triplet Excitation-Energy Transfer Couplings from Subsystem Time-Dependent Density-Functional Theory J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-07 Sabine Käfer, Niklas Niemeyer, Johannes Tölle, Johannes Neugebauer
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Three-State Diffusion Model of DNA Glycosylase Translocation along Stretched DNA as Revealed by Free Energy Landscapes at the All-Atom Level J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-07 Hyeonjun Kim, Youngshang Pak
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Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots? J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-07 Gabriel Oanca, Johan Åqvist
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Role of Singles Amplitudes in ADC(2) and CC2 for Low-Lying Electronically Excited States J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-06 Niklas Sülzner, Christof Hättig
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Switching Go̅-Martini for Investigating Protein Conformational Transitions and Associated Protein–Lipid Interactions J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-06 Song Yang, Chen Song
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Comprehensive Comparison and Critical Assessment of RNA-Specific Force Fields J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-06 Taeyoung Choi, Zhengxin Li, Ge Song, Hai-Feng Chen
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Systematic DFT Modeling van der Waals Heterostructures from a Complete Configurational Basis Applied to γ-PC/WS2 J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-06 Joran Celis, Wei Cao
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Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-06 Rika Tandiana, German P. Barletta, Miguel Angel Soler, Sara Fortuna, Walter Rocchia
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Fragment-Based Deep Learning for Simultaneous Prediction of Polarizabilities and NMR Shieldings of Macromolecules and Their Aggregates J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-05 Dongbo Zhao, Yilin Zhao, Enhua Xu, Wenqi Liu, Paul W. Ayers, Shubin Liu, Dahua Chen
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Modeling Fe(II) Complexes Using Neural Networks J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-05 Hongni Jin, Kenneth M. Merz, Jr.
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Accelerating Analytic-Continuation GW Calculations with a Laplace Transform and Natural Auxiliary Functions J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-04 Johannes Tölle, Niklas Niemeyer, Johannes Neugebauer
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Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-03-01 Wojciech Plazinski, Valery Lutsyk, Anita Plazinska
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RT-EOM-CCSD Calculations of Inner and Outer Valence Ionization Energies and Spectral Functions J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-29 Fernando D. Vila, John J. Rehr, Karol Kowalski, Bo Peng
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Relative Resolution: An Analysis with the Kullback–Leibler Entropy J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-28 Mark Chaimovich, Aviel Chaimovich
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Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-28 Jiahua Deng, Qiang Cui
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Introduction to Computational and Theoretical Studies Focused on Self-Assembly and Molecular Organization J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-27 Fernando A. Escobedo, Amir Haji-Akbari, Sumit Sharma
This article is part of the Computational and Theoretical Studies Focused on Self-Assembly and Molecular Organization special issue. Self-assembly refers to the bottom-up organization of matter into structures with varying degrees and types of order and underpins the formation of materials such as micelles, molecular, polymeric and colloidal crystals, folded biomolecules, and biological organelles
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Earth Mover’s Charge Transfer Distance: A General and Robust Approach for Describing Excited State Locality J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-26 Mathias Fraiponts, Wouter Maes, Benoît Champagne
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When Data Are Lacking: Physics-Based Inverse Design of Biopolymers Interacting with Complex, Fluid Phases J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-27 Jeroen Methorst, Niek van Hilten, Art Hoti, Kai Steffen Stroh, Herre Jelger Risselada
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Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-27 Carlos Roldán-Piñero, Juan Luengo-Márquez, Salvatore Assenza, Rubén Pérez
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Spin-Symmetry Breaking and Hyperfine Couplings in Transition-Metal Complexes Revisited Using Density Functionals Based on the Exact-Exchange Energy Density J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-27 Artur Wodyński, Bryan Lauw, Marc Reimann, Martin Kaupp
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Electrostatics as a Guiding Principle in Understanding and Designing Enzymes J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-27 J. Javier Ruiz-Pernía, Katarzyna Świderek, Joan Bertran, Vicent Moliner, Iñaki Tuñón
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Binding of Carbon Monoxide to Hemoglobin in an Oxygen Environment: Force Field Development for Molecular Dynamics J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-24 Mingrui Jiang, Chi-Hua Yu, Zhiping Xu, Zhao Qin
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Accelerated Lignocellulosic Molecule Adsorption Structure Determination J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-26 Joakim S. Jestilä, Nian Wu, Fabio Priante, Adam S. Foster
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Machine Learning Deciphered Molecular Mechanistics with Accurate Kinetic and Thermodynamic Prediction J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-23 Junlin Dong, Shiyu Wang, Wenqiang Cui, Xiaolin Sun, Haojie Guo, Hailu Yan, Horst Vogel, Zhi Wang, Shuguang Yuan
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Accurate Machine Learning for Predicting the Viscosities of Deep Eutectic Solvents J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-22 Mood Mohan, Karuna Devi Jetti, Micholas Dean Smith, Omar N. Demerdash, Michelle K. Kidder, Jeremy C. Smith
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Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-23 Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo
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Programming Interfacial Porosity and Symmetry with Escherized Colloids J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-22 Nathan A. Mahynski, Vincent K. Shen
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Bayesian Multistate Bennett Acceptance Ratio Methods J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-22 Xinqiang Ding
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Evaluating the Impact of the Tamm–Dancoff Approximation on X-ray Spectrum Calculations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-22 Thomas Fransson, Lars G. M. Pettersson
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Tensor Hypercontraction of Cluster Perturbation Theory: Quartic Scaling Perturbation Series for the Coupled Cluster Singles and Doubles Ground-State Energies J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-21 Andreas Erbs Hillers-Bendtsen, Kurt V. Mikkelsen, Todd J. Martinez
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Renormalized-Residue-Based Multireference Configuration Interaction Method for Strongly Correlated Systems J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-21 Yifan Cheng, Haibo Ma
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Charge-Optimized Electrostatic Interaction Atom-Centered Neural Network Algorithm J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-21 Zichen Song, Jian Han, Graeme Henkelman, Lei Li
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Formic Acid–Ammonia Heterodimer: A New Δ-Machine Learning CCSD(T)-Level Potential Energy Surface Allows Investigation of the Double Proton Transfer J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-21 Paul L. Houston, Chen Qu, Qi Yu, Priyanka Pandey, Riccardo Conte, Apurba Nandi, Joel M. Bowman, Stephen G. Kukolich
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All-Atom Biomolecular Simulation in the Exascale Era J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-21 Thomas L. Beck, Paolo Carloni, Dilipkumar N. Asthagiri
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Solvent Distribution Effects on Quantum Chemical Calculations with Quantum Computers J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-20 Yuichiro Yoshida, Wataru Mizukami, Norio Yoshida
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Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-19 Shu Li, Bohua Wu, Yun Lyna Luo, Wei Han
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Quantum Cluster Equilibrium Theory for Multicomponent Liquids J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-19 Tom Frömbgen, Katrin Drysch, Paul Zaby, Jürgen Dölz, Johannes Ingenmey, Barbara Kirchner
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The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-19 Anna-Lena M. Fischer, Anna Tichy, Janik Kokot, Valentin J. Hoerschinger, Robert F. Wild, Jakob R. Riccabona, Johannes R. Loeffler, Franz Waibl, Patrick K. Quoika, Philipp Gschwandtner, Stefano Forli, Andrew B. Ward, Klaus R. Liedl, Martin Zacharias, Monica L. Fernández-Quintero
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Surface-Accelerated String Method for Locating Minimum Free Energy Paths J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-17 Timothy J. Giese, Şölen Ekesan, Erika McCarthy, Yujun Tao, Darrin M. York
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Coarse-Grained Model of Glycosaminoglycans for Biomolecular Simulations J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-15 Aishwary T. Shivgan, Jan K. Marzinek, Alexander Krah, Paul Matsudaira, Chandra S. Verma, Peter J. Bond
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MACE: Automated Assessment of Stereochemistry of Transition Metal Complexes and Its Applications in Computational Catalysis J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-16 Ivan Yu. Chernyshov, Evgeny A. Pidko
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Hierarchical Assembly of Single-Stranded RNA J. Chem. Theory Comput. (IF 5.5) Pub Date : 2024-02-15 Lisa M. Pietrek, Lukas S. Stelzl, Gerhard Hummer